Voltage-driven DNA translocations through a nanopore.

TLDR: Current blockade and time distributions for single-stranded DNA polymers during voltage-driven translocations through a single alpha-hemolysin pore imply that, while polymers longer than the pore are translocated at a constant speed, the velocity of shorter polymers increases with decreasing length.

Abstract: We measure current blockade and time distributions for single-stranded DNA polymers during voltage-driven translocations through a single alpha-hemolysin pore. We use these data to determine the velocity of the polymers in the pore. Our measurements imply that, while polymers longer than the pore are translocated at a constant speed, the velocity of shorter polymers increases with decreasing length. This velocity is nonlinear with the applied field. Based on this data, we estimate the effective diffusion coefficient and the energy penalty for extending a molecule into the pore.

Figures

FIG. 2. The most probable blockade level, IP , as a function of N for poly(dA). IP depends weakly on N for long polymers N . 12 . In contrast, IP has a steep dependence on N for shorter polymers N , 12 . The transition point N 12 corresponds to polymer contour length of 48 Å. Inset: IP is extracted from the translocation blockade distribution of the individual events, which is well fit by a Gaussian function. Error bars (standard error of the mean) are determined by evaluating IP for 3–5 data sets of the same polymer. The line is drawn to guide the eye.

FIG. 1. (a) Single-stranded DNA molecules (negatively charged) and salt ions are electrically driven through a single a-hemolysin protein pore embedded in a phospholipid membrane. Most of the ionic current through the pore is blocked during DNA passage. (b) Three representative translocation current blockades are shown for 15mer (“1” and “2”) and for 7mer (“3”) poly(dA). For each event we measured the translocation time, tD , and the average event blockade, IB .

FIG. 4. The dependence of polymer velocity on the applied voltage is nonlinear. Data shown for N 12 and N 30 poly(dA)s at 2 ±C. The lines are quadratic fits to the data (see text). Error bars are determined as in Fig. 2, except for points below 90 mV where the number of events is insufficient to determine the error bars. Inset: Estimated upper bound values for the effective diffusion coefficient, Dmax, based on the polymers’ velocity.

FIG. 3. Inset: A typical translocation time histogram of 1000 events showing a non-Gaussian distribution with a peak defined as tP and exponential tail. The width of the distribution is defined at tPe21 2. Main figure: tP is used to evaluate the apparent velocity and the corrected velocity , as a function of N . Both velocities are constant for N . 12, with a typical plateau value of 0.15 Å ms at 2 ±C and 120 mV. Short polymers N , 12 move significantly faster through the pore than their longer counterparts. Error bars are determined as in Fig. 2. Lines are drawn to guide the eye.